ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data
Bioconductor version: Release (3.19)
The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities.
Author: Lihua Julie Zhu, Jianhong Ou, Jun Yu, Kai Hu, Haibo Liu, Junhui Li, Hervé Pagès, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe, Michael Green
Maintainer: Jianhong Ou <jianhong.ou at duke.edu>, Lihua Julie Zhu <julie.zhu at umassmed.edu>, Kai Hu <kai.hu at umassmed.edu>, Junhui Li <junhui.li at umassmed.edu>
citation("ChIPpeakAnno")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChIPpeakAnno")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPpeakAnno")| ChIPpeakAnno: annotate, visualize, and compare peak data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, ChIPSeq, ChIPchip, Software |
| Version | 3.38.1 |
| In Bioconductor since | BioC 2.5 (R-2.10) (15 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.5), methods, IRanges(>= 2.13.12), GenomicRanges(>= 1.31.8), S4Vectors(>= 0.17.25) |
| Imports | AnnotationDbi, BiocGenerics(>= 0.1.0), Biostrings(>= 2.47.6), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils, universalmotif, stringr, tibble, tidyr, data.table, scales, ensembldb |
| System Requirements | |
| URL |
See More
| Suggests | AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack, OrganismDbi, BiocFileCache |
| Linking To | |
| Enhances | |
| Depends On Me | REDseq, csawBook |
| Imports Me | ATACseqQC, DEScan2, GUIDEseq |
| Suggests Me | R3CPET, hicVennDiagram, seqsetvis, chipseqDB |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChIPpeakAnno_3.38.1.tar.gz |
| Windows Binary (x86_64) | ChIPpeakAnno_3.38.1.zip |
| macOS Binary (x86_64) | ChIPpeakAnno_3.38.0.tgz |
| macOS Binary (arm64) | ChIPpeakAnno_3.38.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ChIPpeakAnno |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ChIPpeakAnno |
| Bioc Package Browser | https://code.bioconductor.org/browse/ChIPpeakAnno/ |
| Package Short Url | https://bioconductor.org/packages/ChIPpeakAnno/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |